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- PDB-9uza: Crystal structure of Crimean-Congo hemorrhagic fever virus cap-sn... -

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Basic information

Entry
Database: PDB / ID: 9uza
TitleCrystal structure of Crimean-Congo hemorrhagic fever virus cap-snatching endonuclease
Components
  • RNA-directed RNA polymerase L
  • mAb G5 Fab heavy chain
  • mAb G5 Fab light chain
KeywordsHYDROLASE / cap-snatching endonuclease
Function / homology
Function and homology information


protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / viral RNA genome replication ...protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription
Similarity search - Function
RNA-directed RNA polymerase, nairovirus / : / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesOrthonairovirus haemorrhagiae
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsDeng, Z. / Kuang, W. / Tian, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structure and function of the nairovirus cap-snatching endonuclease
Authors: Kuang, W. / Tian, Z. / Zhang, G. / Wu, F. / Li, J. / Tang, J. / Zhang, H. / Zhuo, X. / Hu, Z. / Wang, M. / Zhao, H. / Deng, Z.
History
DepositionMay 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
H: mAb G5 Fab heavy chain
L: mAb G5 Fab light chain
B: RNA-directed RNA polymerase L
C: mAb G5 Fab heavy chain
D: mAb G5 Fab light chain


Theoretical massNumber of molelcules
Total (without water)170,8066
Polymers170,8066
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.767, 99.779, 180.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-directed RNA polymerase L / Large structural protein / Replicase / Transcriptase


Mass: 36555.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthonairovirus haemorrhagiae / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D5MEH7, RNA-directed RNA polymerase, ubiquitinyl hydrolase 1
#2: Antibody mAb G5 Fab heavy chain


Mass: 24788.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody mAb G5 Fab light chain


Mass: 24058.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 2% vol/vol TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, and 20% wt/vol Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.04→90.21 Å / Num. obs: 35085 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.062 / Rrim(I) all: 0.161 / Net I/σ(I): 5.1
Reflection shellResolution: 3.04→3.21 Å / Redundancy: 13.6 % / Num. unique obs: 5038 / CC1/2: 0.434 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→29.11 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.295 1768 5.13 %
Rwork0.2255 --
obs0.2291 34469 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10709 0 0 0 10709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310963
X-RAY DIFFRACTIONf_angle_d1.61914882
X-RAY DIFFRACTIONf_dihedral_angle_d6.1671450
X-RAY DIFFRACTIONf_chiral_restr0.0781669
X-RAY DIFFRACTIONf_plane_restr0.0131902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.130.46891140.43852434X-RAY DIFFRACTION97
3.13-3.220.42041330.42479X-RAY DIFFRACTION99
3.22-3.330.39331350.37072478X-RAY DIFFRACTION100
3.33-3.450.42431360.34312472X-RAY DIFFRACTION100
3.45-3.580.41611450.30592498X-RAY DIFFRACTION100
3.58-3.750.34351410.28782499X-RAY DIFFRACTION100
3.75-3.940.32731280.27822504X-RAY DIFFRACTION100
3.95-4.190.35231400.26592497X-RAY DIFFRACTION100
4.19-4.510.35311310.22842533X-RAY DIFFRACTION100
4.51-4.970.24641400.22052526X-RAY DIFFRACTION100
4.97-5.680.2911280.21142542X-RAY DIFFRACTION100
5.68-7.140.28611420.22732598X-RAY DIFFRACTION100
7.14-29.110.23271550.15362641X-RAY DIFFRACTION99

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